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Last data update: 2014.03.03
BiocGenerics

Package: BiocGenerics
Title: S4 generic functions for Bioconductor
Description: S4 generic functions needed by many Bioconductor packages.
Version: 0.18.0
Author: The Bioconductor Dev Team
Maintainer: Bioconductor Package Maintainer <maintainer@bioconductor.org>
biocViews: Infrastructure
Depends: methods, utils, graphics, stats, parallel
Imports: methods, utils, graphics, stats, parallel
Suggests: Biobase, S4Vectors, IRanges, GenomicRanges, AnnotationDbi,
oligoClasses, oligo, affyPLM, flowClust, affy, DESeq2, MSnbase,
annotate, RUnit
License: Artistic-2.0
Collate: S3-classes-as-S4-classes.R normarg-utils.R replaceSlots.R
append.R as.data.frame.R as.list.R as.vector.R cbind.R
do.call.R duplicated.R eval.R Extremes.R funprog.R get.R grep.R
is.unsorted.R lapply.R lengths.R mapply.R match.R nrow.R
order.R paste.R rank.R rep.R row_colnames.R sets.R sort.R
start.R subset.R table.R tapply.R unique.R unlist.R unsplit.R
relist.R boxplot.R image.R density.R IQR.R mad.R residuals.R
weights.R xtabs.R clusterApply.R annotation.R combine.R
dbconn.R dge.R fileName.R normalize.R organism_species.R
plotMA.R plotPCA.R score.R strand.R updateObject.R
testPackage.R zzz.R
NeedsCompilation: no
Packaged: 2016-05-04 04:18:48 UTC; biocbuild
● BiocViews: Infrastructure
● 4 images, 57 functions, 0 datasets
● Reverse Depends: 100
Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'BiocGenerics' ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for 'append' in package 'BiocGenerics'
Creating a new generic function for 'as.data.frame' in package 'BiocGenerics'
Creating a new generic function for 'cbind' in package 'BiocGenerics'
Creating a new generic function for 'rbind' in package 'BiocGenerics'
Creating a new generic function for 'do.call' in package 'BiocGenerics'
Creating a new generic function for 'duplicated' in package 'BiocGenerics'
Creating a new generic function for 'anyDuplicated' in package 'BiocGenerics'
Creating a new generic function for 'eval' in package 'BiocGenerics'
Creating a new generic function for 'pmax' in package 'BiocGenerics'
Creating a new generic function for 'pmin' in package 'BiocGenerics'
Creating a new generic function for 'pmax.int' in package 'BiocGenerics'
Creating a new generic function for 'pmin.int' in package 'BiocGenerics'
Creating a new generic function for 'Reduce' in package 'BiocGenerics'
Creating a new generic function for 'Filter' in package 'BiocGenerics'
Creating a new generic function for 'Find' in package 'BiocGenerics'
Creating a new generic function for 'Map' in package 'BiocGenerics'
Creating a new generic function for 'Position' in package 'BiocGenerics'
Creating a new generic function for 'get' in package 'BiocGenerics'
Creating a new generic function for 'mget' in package 'BiocGenerics'
Creating a new generic function for 'grep' in package 'BiocGenerics'
Creating a new generic function for 'grepl' in package 'BiocGenerics'
Creating a new generic function for 'is.unsorted' in package 'BiocGenerics'
Creating a new generic function for 'lapply' in package 'BiocGenerics'
Creating a new generic function for 'sapply' in package 'BiocGenerics'
Creating a new generic function for 'lengths' in package 'BiocGenerics'
Creating a new generic function for 'mapply' in package 'BiocGenerics'
Creating a new generic function for 'match' in package 'BiocGenerics'
Creating a new generic function for 'order' in package 'BiocGenerics'
Creating a new generic function for 'paste' in package 'BiocGenerics'
Creating a new generic function for 'rank' in package 'BiocGenerics'
Creating a new generic function for 'rownames' in package 'BiocGenerics'
Creating a new generic function for 'colnames' in package 'BiocGenerics'
Creating a new generic function for 'union' in package 'BiocGenerics'
Creating a new generic function for 'intersect' in package 'BiocGenerics'
Creating a new generic function for 'setdiff' in package 'BiocGenerics'
Creating a new generic function for 'sort' in package 'BiocGenerics'
Creating a new generic function for 'table' in package 'BiocGenerics'
Creating a new generic function for 'tapply' in package 'BiocGenerics'
Creating a new generic function for 'unique' in package 'BiocGenerics'
Creating a new generic function for 'unsplit' in package 'BiocGenerics'
Creating a new generic function for 'IQR' in package 'BiocGenerics'
Creating a new generic function for 'mad' in package 'BiocGenerics'
Creating a new generic function for 'xtabs' in package 'BiocGenerics'
Creating a new generic function for 'clusterCall' in package 'BiocGenerics'
Creating a new generic function for 'clusterApply' in package 'BiocGenerics'
Creating a new generic function for 'clusterApplyLB' in package 'BiocGenerics'
Creating a new generic function for 'clusterEvalQ' in package 'BiocGenerics'
Creating a new generic function for 'clusterExport' in package 'BiocGenerics'
Creating a new generic function for 'clusterMap' in package 'BiocGenerics'
Creating a new generic function for 'parLapply' in package 'BiocGenerics'
Creating a new generic function for 'parSapply' in package 'BiocGenerics'
Creating a new generic function for 'parApply' in package 'BiocGenerics'
Creating a new generic function for 'parRapply' in package 'BiocGenerics'
Creating a new generic function for 'parCapply' in package 'BiocGenerics'
Creating a new generic function for 'parLapplyLB' in package 'BiocGenerics'
Creating a new generic function for 'parSapplyLB' in package 'BiocGenerics'
** help
*** installing help indices
  converting help for package 'BiocGenerics'
    finding HTML links ... done
    BiocGenerics-package                    html  
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    Extremes                                html  
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    IQR                                     html  
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    S3-classes-as-S4-classes                html  
    annotation                              html  
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    append                                  html  
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    as.data.frame                           html  
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    as.vector                               html  
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    boxplot                                 html  
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    cbind                                   html  
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    clusterApply                            html  
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    combine                                 html  
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    dbconn                                  html  
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    density                                 html  
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    dge                                     html  
    do.call                                 html  
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    duplicated                              html  
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    eval                                    html  
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    evalq                                   html  
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    residuals                               html  
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    row_colnames                            html  
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/row_colnames.Rd:66: missing file link 'selectMethod'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/score.Rd:34: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/score.Rd:37: missing file link 'score,GenomicRanges-method'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/score.Rd:39: missing file link 'GenomicRanges'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sets.Rd:17: missing file link 'union'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sets.Rd:39: missing file link 'union'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sets.Rd:57: missing file link 'GRanges'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sets.Rd:65: missing file link 'union'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sets.Rd:71: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sets.Rd:74: file link 'union,GRanges,GRanges-method' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sets.Rd:76: missing file link 'GRanges'
    sort                                    html  
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sort.Rd:62: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sort.Rd:65: missing file link 'sort,Vector-method'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/sort.Rd:67: missing file link 'Vector'
    start                                   html  
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/start.Rd:57: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/start.Rd:60: missing file link 'start,IRanges-method'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/start.Rd:62: missing file link 'IRanges'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/strand.Rd:73: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/strand.Rd:76: missing file link 'strand,GRanges-method'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/strand.Rd:78: missing file link 'GRanges'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/subset.Rd:46: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/subset.Rd:49: missing file link 'subset,DataTable-method'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/table.Rd:46: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/table.Rd:49: missing file link 'table,Rle-method'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/table.Rd:51: missing file link 'Rle'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/tapply.Rd:64: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/tapply.Rd:67: missing file link 'tapply,Vector,ANY-method'
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    testPackage                             html  
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unique.Rd:57: missing file link 'selectMethod'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unlist.Rd:51: missing file link 'selectMethod'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unlist.Rd:56: missing file link 'List'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unsplit.Rd:14: missing file link 'unsplit'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unsplit.Rd:33: missing file link 'unsplit'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unsplit.Rd:39: missing file link 'unsplit'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unsplit.Rd:48: missing file link 'unsplit'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unsplit.Rd:54: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unsplit.Rd:57: missing file link 'unsplit,List-method'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/unsplit.Rd:59: missing file link 'List'
    updateObject                            html  
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/updateObject.Rd:130: missing file link 'selectMethod'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/weights.Rd:47: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/weights.Rd:50: missing file link 'weights,PLMset-method'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/weights.Rd:52: missing file link 'PLMset'
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Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/xtabs.Rd:51: missing file link 'selectMethod'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/xtabs.Rd:54: missing file link 'xtabs,DataTable-method'
Rd warning: /tmp/RtmpRyckK7/R.INSTALL4f8348f968d3/BiocGenerics/man/xtabs.Rd:56: missing file link 'DataTable'
** building package indices
** testing if installed package can be loaded
* DONE (BiocGenerics)
Making 'packages.html' ... done